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1. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Author

Bastien Mérigot, Anne Chenuil, Sophie Dubois, Jean-Baptiste Ledoux, Emilie Boissin, Abigail E. Cahill, Didier Aurelle, Alexandra Anh-Thu Weber, Zoheir Bouzaza, Emilie Egea, Olivier Chabrol, Aurélien De Jode, Romain David, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Université Abdelhamid Ibn Badis de Mostaganem, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Institut de Mathématiques de Marseille (I2M), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD [France-Ouest]), University of Basel (Unibas), Aix-Marseille Université, Fundação para a Ciência e a Tecnologia (Portugal), Université Abdelhamid Ibn Badis Mostaganem, European Commission, Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), Evolutionary Biology and Ecology of Algae ( EBEA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Pontificia Universidad Católica de Chile-Universidad Austral de Chile-Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherches insulaires et observatoire de l'environnement ( CRIOBE ), Université de Perpignan Via Domitia ( UPVD ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Excellence CORAIL ( LabEX CORAIL ), Institut de Recherche pour le Développement ( IRD ) -Université des Antilles et de la Guyane ( UAG ) -École des hautes études en sciences sociales ( EHESS ) -École pratique des hautes études ( EPHE ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de la Réunion ( UR ) -Université de la Polynésie Française ( UPF ) -Université de Nouvelle Calédonie-Institut d'écologie et environnement, Institut de Mathématiques de Marseille ( I2M ), Aix Marseille Université ( AMU ) -Ecole Centrale de Marseille ( ECM ) -Centre National de la Recherche Scientifique ( CNRS ), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] ( ICM ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Centro Interdisciplinar de Investigação Marinha e Ambiental ( CIMAR/CIIMAR ), Universidade do Porto [Porto], MARine Biodiversity Exploitation and Conservation ( UMR MARBEC ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Institut de Recherche pour le Développement ( IRD [France-Ouest] ), University of Basel ( Unibas ), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Aquatic Organisms, Population, Biology, Population structure, 010603 evolutionary biology, 01 natural sciences, Population density, Genetic diversity, Larvae, Mediterranean Sea, Genetics, Animals, 14. Life underwater, education, Species genetic diversity correlation, Ecology, Evolution, Behavior and Systematics, Invertebrate, education.field_of_study, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Geography, Ecology, Marine invertebrates, 010604 marine biology & hydrobiology, Marine larval ecology, Genetic Variation, Species diversity, Biodiversity, Dispersal, 15. Life on land, Invertebrates, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetics, Population, 13. Climate action, Larva, Genetic structure, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution, human activities
Abstract

Cahill, Abigail E. ... et al.-- 15 pages, 5 figures, 4 tables, supporting information https://dx.doi.org/10.1111/mec.14389, data accessibility in GenBank (accession nos MG063882–MG064453), DataDryad https://doi.org/10.5061/dryad.dv4 mg, GitHub https://github.com/chaby/dana, Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies, Funding was provided by DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status), funded by the European Union under the 7th FRAMEWORK Programme, “The Ocean of Tomorrow” (grant agreement no. 308392), www.devotes-project.eu, and by La Faculté des Sciences de la Nature et de la Vie de l’Université Abdelhamid Ibn Badis, Mostaganem, Algeria (ZB) and the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia; FCT; Postdoctoral grant SFRH/BPD/74400/2010; JBL). This work is a contribution to Labex OT-Med (n° ANR-11-LABX-0061) and has received funding from Excellence Initiative of Aix-Marseille University - A*MIDEX, a French “Investissements d’Avenir” programme”

Published
2017

2. Multiple regression analysis to assess the spatial distribution and speciation of mercury in surface sediments of a contaminated lagoon

Author

David Amouroux, M.G. Lobos Valenzuela, M.E. Pereira, João P. Coelho, Emmanuel Tessier, Teodor Stoichev, Centro Interdisciplinar de Investigação Marinha e Ambiental CIMAR /CIIMAR, Universidade do Porto, Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Valparaiso University, and European SUDOE Interreg IVB Programm FONDECYT project (1150855)

Subjects
Environmental Engineering, Health, Toxicology and Mutagenesis, Multiple regression model, 0211 other engineering and technologies, chemistry.chemical_element, 02 engineering and technology, 010501 environmental sciences, Isotope dilution, 01 natural sciences, Sediments, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Environmental Chemistry, Organic matter, Mercury species, Water pollution, Waste Management and Disposal, Methylmercury, 0105 earth and related environmental sciences, chemistry.chemical_classification, 021110 strategic, defence & security studies, Chlor-alkali industry, Sediment, [CHIM.MATE]Chemical Sciences/Material chemistry, Contamination, Coastal lagoon, Pollution, 6. Clean water, Mercury (element), [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, Environmental chemistry, Environmental science, Water quality
Abstract

International audience; The concentrations of inorganic mercury (IHg) and methylmercury (MeHg) in surface sediments from the contaminated Aveiro Lagoon (Portugal) were determined by species-specific isotope dilution analysis. Different behaviour of IHg and MeHg was observed based upon multiple regression analysis, including geochemical characteristics of the surface sediments (fine fraction, concentrations of organic matter and metals) and non-Euclidean distances between sampling points. This data treatment method was valid over the entire concentration range of IHg and MeHg, allowing robust quantitative evaluation with respect to extrapolation. For IHg, there was statistical separation of the dispersion away from the contamination source and of Al concentration in the sediments. The MeHg concentrations followed those of IHg at high concentrations. The geochemical variables, such as concentrations of Ca (marine influence proxy), Mn and organic matter, were necessary to describe the behaviour of MeHg across the whole concentration range. The models for MeHg demonstrated that, close to the mouth of the lagoon, net production of MeHg was higher. In future, multiple regression analysis could be applied to separate and to evaluate quantitatively the effects of geochemistry and dispersion away from the contamination source in sediments contaminated with other substances.

Published
2019

3. Exopolysaccharides from Cyanobacteria: Strategies for Bioprocess Development

Author

Vitor Vasconcelos, Diogo Cruz, Cédric Delattre, Philippe Michaud, Guillaume Pierre, Faculty of Sciences of the University of Porto (FCUP), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto = University of Porto, Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Centro Interdisciplinar de Investigação Marinha e Ambiental, and Universidade do Porto

Subjects
0106 biological sciences, Cyanobacteria, Exopolysaccharides, Computer science, lcsh:Technology, 01 natural sciences, cyanobacteria, lcsh:Chemistry, 03 medical and health sciences, 010608 biotechnology, General Materials Science, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Bioprocess, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], lcsh:QH301-705.5, Instrumentation, 030304 developmental biology, Fluid Flow and Transfer Processes, 0303 health sciences, Downstream processing, biology, lcsh:T, Process Chemistry and Technology, exopolysaccharides, General Engineering, bioprocess, biology.organism_classification, lcsh:QC1-999, Computer Science Applications, lcsh:Biology (General), lcsh:QD1-999, lcsh:TA1-2040, 13. Climate action, Biochemical engineering, lcsh:Engineering (General). Civil engineering (General), lcsh:Physics
Abstract

Cyanobacteria have the potential to become an industrially sustainable source of functional biopolymers. Their exopolysaccharides (EPS) harbor chemical complexity, which predicts bioactive potential. Although some are reported to excrete conspicuous amounts of polysaccharides, others are still to be discovered. The production of this strain-specific trait can promote carbon neutrality while its intrinsic location can potentially reduce downstream processing costs. To develop an EPS cyanobacterial bioprocess (Cyano-EPS) three steps were explored: the selection of the cyanobacterial host; optimization of production parameters; downstream processing. Studying the production parameters allow us to understand and optimize their response in terms of growth and EPS production though many times it was found divergent. Although the extraction of EPS can be achieved with a certain degree of simplicity, the purification and isolation steps demand experience. In this review, we gathered relevant research on EPS with a focus on bioprocess development. Challenges and strategies to overcome possible drawbacks are highlighted. This research was funded by FCT UIDB/04423/2020 and UIDP/04423/2020 and by the Atlantic Interreg Project Enhance MicroAlgae - High added-value industrial opportunities for microalgae in the Atlantic Area [EAPA_338/2016].

Published
2020

4. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader

Author

Manuel Ferrer, Alexander J. Mann, Hanno Teeling, Tran Hai, Peter N. Golyshin, Marco Taborda, Johannes Werner, Frank Oliver Glöckner, Silvia Juárez, Olga V. Golyshina, Violetta La Cono, Milton S. da Costa, Gurvan Michel, Sergio Ciordia, André Antunes, Sixing Huang, María Alcaide, Michail M. Yakimov, Juan Pablo Albar, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Association pour la Formation Professionnelle des Adultes (AFPA), Association pour la Formation Professionnelle des Adultes, Princeton University, Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Proteomics facility, Centro Nacional de Biotecnología, Insitute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche (CNR), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, Departamento de Biologia, Institute for Biotechnology and Bioengineering (IBB), Technical University of Lisbon, Universidade de Coimbra [Coimbra], State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences [Beijing], Sino-French Laboratory LABIOCEM, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, School of Biological Sciences [Bangor], Bangor University, European Commission, Ministerio de Economía y Competitividad (España), Max Planck Society, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto = University of Porto, Universidade do Minho, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), and Universidade do Porto [Porto]

Subjects
MESH: Genome, Archaeal, [SDV]Life Sciences [q-bio], MESH: Indian Ocean, Sodium Chloride, Genome, Archaeal, Utah, Glycoside hydrolase, MESH: Ecosystem, Anaerobiosis, MESH: Phylogeny, Indian Ocean, extremophiles, Research Articles, Phylogeny, 0303 health sciences, Halobacteriaceae, biology, Ecology, Salt Tolerance, Anoxic waters, Adaptation, Physiological, Biological Evolution, Halorhabdus, Proteome, MESH: Lakes, MESH: Metagenomics, Water Microbiology, MESH: Oxygen, MESH: Sodium Chloride, Glycoside Hydrolases, MESH: Biological Evolution, Microbiology, 03 medical and health sciences, MESH: Halobacteriaceae, Phylogenetics, MESH: Enzyme Assays, Polysaccharides, Botany, MESH: Anaerobiosis, MESH: Glycoside Hydrolases, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, Enzyme Assays, Science & Technology, MESH: Salt-Tolerance, 030306 microbiology, Thermophile, MESH: Utah, deep sea brine, biology.organism_classification, MESH: Adaptation, Physiological, MESH: Water Microbiology, Oxygen, Lakes, MESH: Polysaccharides, euryarchaeon, 13. Climate action, Metagenomics, Archaea
Abstract

Summary: Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensisAX-2T from the shallow Great Salt Lake of Utah, and Halorhabdus tiamateaSARL4BT from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H.tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H.tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H.tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments., This study was supported by the EU FP7 project MAMBA (‘Marine Metagenomics for New Biotechnological Applications’, FP7‐KBBE‐2008–226977, the Spanish Ministry of Economy and Competitiveness (grant BIO2011–25012) and the Max Planck Society. H.T., O.V.G. and P.N.G. acknowledge the support of EU FP7 for the project MicroB3 (OCEAN‐2011‐287589).

Published
2014

5. Harvesting effects, recovery mechanisms, and management strategies for a long-lived and structural precious coral

Author

Montero-Serra, Ignasi, Linares, Cristina, García, Marina, Pancaldi, Francesca, Frleta-Valić, Maša, Ledoux, J. B., Zuberer, F., Merad, Djamel, Drap, Pierre, Garrabou, Joaquim, Universitat de Barcelona, Departament d'Ecologia, Universitat de Barcelona (UB), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Centro Interdisciplinar de Investigação Marinha e Ambiental CIMAR /CIIMAR, Universidade do Porto [Porto], Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidade do Porto = University of Porto, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto, Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut de Recherche pour le Développement (IRD), and Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU)

Subjects
LIFE-HISTORY, CONSERVATION, lcsh:Medicine, Ecologia marina, Marine ecology, RED CORAL, ECOSYSTEMS, Mortalitat, Animals, Humans, Mortality, lcsh:Science, Coralls, DECLINE, MASS MORTALITY, lcsh:R, Anthozoa, REPRODUCTION, INSIGHTS, RUBRUM POPULATIONS, MARINE FOOD WEBS, [SDE]Environmental Sciences, Pesca, Corals, lcsh:Q, Fishing, Research Article
Abstract

14 pages, 5 figures, supporting information http://dx.doi.org/10.1371/journal.pone.0117250, Overexploitation is a major threat for the integrity of marine ecosystems. Understanding the ecological consequences of different extractive practices and the mechanisms underlying the recovery of populations is essential to ensure sustainable management plans. Precious corals are long-lived structural invertebrates, historically overfished, and their conservation is currently a worldwide concern. However, the processes underlying their recovery are poorly known. Here, we examined harvesting effects and recovery mechanisms of red coral Corallium rubrum by analyzing long-term photographic series taken on two populations that were harvested. We compared the relative importance of reproduction and re-growth as drivers of resilience. Harvesting heavily impacted coral populations causing large decreases in biomass and strong size-class distribution shifts towards populations dominated by small colonies. At the end of the study (after 4 and 7 years) only partial recovery was observed. The observed general pattern of low recruitment and high mortality of new recruits demonstrated limited effects of reproduction on population recovery. Adversely, low mortality of partially harvested adults and a large proportion of colonies showing new branches highlighted the importance of re-growth in the recovery process. The demographic projections obtained through stochastic models confirmed that the recovery rates of C. rubrum can be strongly modulated depending on harvesting procedures. Thus, leaving the basal section of the colonies when harvesting to avoid total mortality largely enhances the resilience of C. rubrum populations and quickens their recovery. On the other hand, the high survival of harvested colonies and the significant biomass reduction indicated that abundance may not be an adequate metric to assess the conservation status of clonal organisms because it can underestimate harvesting effects. This study highlights the unsustainability of current harvesting practices of C. rubrum and provides urgently needed data to improve management practices that are still largely based on untested assumptions. © 2015 Montero-Serra et al., Support for this work was provided by a FPI grant (BES-2013-066150) to I. Montero-Serra and by a Ramon y Cajal research contract (RyC-2011-08134) to C. Linares. This study was partially funded by the Spanish Ministry of Economy and Innovation Biorock project (CTM2009-08045) and Smart project (CGL2012-32194). The authors are part of the Marine Conservation research group (2009 SGR 1174) from the Generalitat de Catalunya

6. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species.

Author

Galpert D, Del Río S, Herrera F, Ancede-Gallardo E, Antunes A, and Agüero-Chapin G

Subjects
Algorithms, Databases, Nucleic Acid, Genes, Fungal, Sequence Analysis, DNA methods, Yeasts genetics
Abstract

Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles) are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

Published
2015
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